r-genetics and galaxy
We have some tools that I think have been put into an R package but not sent to CRAN. They implement the methods in http://onlinelibrary.wiley.com/resolve/doi/pdf?DOI=10.1002/gepi.20516 This has been used for data sets up to 16000 people x 1M SNPs. I will check to see the current status of the code -- the plan is to refactor it and combine with our analysis code for a Bioconductor package. -thomas
On Sat, 11 Sep 2010, Ross wrote:
Hi Brad Work on the rgenetics tools in R has more or less come to a halt - I'm not aware of anyone working on them and I don't think many people are using them although we tried hard! I think David Clayton's package snpMatrix can handle large datasets but it's something of a struggle to fit billions of genotypes efficiently into the R memory model. For me personally, a bigger problem is enabling the Faculty and biologists I support to work reproducibly without having to worry about the technical problems of hundreds of GB of data. Galaxy really helps with those goals so I've shifted my effort to that framework. The Galaxy tools do use R and BioC under the hood where they're the best solution - but for SNP QC, Plink seems more appropriate because it has the specialized reporting we needed. On Sat, Sep 11, 2010 at 6:00 AM, <r-sig-genetics-request at r-project.org> wrote:
Message: 2
Date: Fri, 10 Sep 2010 16:54:46 -0700
From: Brad McNeney <mcneney at cs.sfu.ca>
To: r-sig-genetics at r-project.org
Subject: Re: [R-sig-genetics] R-sig-genetics Digest, Vol 8, Issue 2
Message-ID: <4C8AC546.6080503 at stat.sfu.ca>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Ross,
Thanks for this. ?I take it then that the QC tools you have in Galaxy
are not in any of the Bioconductor Genetics{Base,Design,Ped} packages?
If not, are there plans to update the Bioconductor packages?
Cheers,
Brad
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Brad McNeney
Statistics and Actuarial Science
Simon Fraser University
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Thomas Lumley Professor of Biostatistics University of Washington, Seattle